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bioRxiv · 10.1101/2021.11.30.470527

sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs

Di Gioacchino, A.·Legendre, R.·Rahou, Y.·Najburg, V.·Charneau, P.·Greenbaum, B. D.·Tangy, F.·van der Werf, S.·Cocco, S.·Komarova, A. V.
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Abstract

Coronavirus RNA-dependent RNA polymerases produce subgenomic RNAs (sgRNAs) that encode viral structural and accessory proteins. User-friendly bioinformatic tools to detect and quantify sgRNA production are urgently needed to study the growing number of next-generation sequencing (NGS) data of SARS-CoV-2. We introduced sgDI-tector to identify and quantify sgRNA in SARS-CoV-2 NGS data. sgDI-tector allowed detection of sgRNA without initial knowledge of the transcription-regulatory sequences. We produced NGS data and successfully detected the nested set of sgRNAs with the ranking M>ORF3a>N>ORF6>ORF7a>ORF8>S>E>ORF7b. We also compared the level of sgRNA production with other types of viral RNA products such as defective interfering viral genomes.

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Di Gioacchino, A., Legendre, R., Rahou, Y., Najburg, V., Charneau, P., Greenbaum, B. D., Tangy, F., van der Werf, S., Cocco, S., Komarova, A. V.. 2021-11-30. sgDI-tector: defective interfering viral genome bioinformatics for detection of coronavirus subgenomic RNAs. https://doi.org/10.1101/2021.11.30.470527

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